EPSPSregulates cell elongation by disrupting the balance of lignin and flavonoid biosynthesis in cotton

EPSPSis a key gene in the shikimic acid synthesis pathway that has been widely used in breeding crops with herbicide resistance. However, its role in regulating cell elongation is poorly understood. Through the overexpression of EPSPSgenes, we generated lines resistant to glyphosate that exhibit an unexpected dwarf phenotype. A representative line, DHR1, exhibits a stable dwarf phenotype throughout its entire growth period. Except for plant height, the other agronomic traits of DHR1are similar to its transgenic explants ZM24. Paraffin section observations showed that DHR1internodes are shortened due to reduced elongation and division of the internode cells. Exogenous hormones confirmed that DHR1is not a classical brassinolide (BR)- or gibberellin (GA)-related dwarfing mutant. Hybridization analysis and fine mapping confirmed that the EPSPSgene is the causal gene for dwarfism, and the phenotype can be inherited in different genotypes. Transcriptome and metabolome analyses showed that genes associated with the phenylpropanoid synthesis pathway are enriched in DHR1compared with ZM24. Flavonoid metabolites are enriched in DHR1, whereas lignin metabolites are reduced. The enhancement of flavonoids likely results in differential expression of auxin signal pathway genes and alters the auxin response, subsequently affecting cell elongation. This study provides a new strategy for generating dwarfs and will accelerate advancements in light simplification in the cultivation and mechanized harvesting of cotton.